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Spring 2013
Instructor: Michael Hagan, Abelson 347; E-mail: hagan@brandeis.edu
Office Hours: 3-5PM, Thursday, or by appointment.
Meeting Time and Place: TBA.
Required course work:
Homework will be handed out in class, usually one every two weeks. Expect fairly extensive
reading assignments. A term paper will be due at the last day of classes. There will be no
written exams, but you will be asked to prepare a short presentation on your term paper
topic at the end of the semester.
Grading Procedure:
50% Homework. 30% Term paper. 20% Presentation.
Please note: problem sets will involve modifying and even writing some Matlab programs, and
typically cannot be completed in a single day. Don't procrastinate -- problem sets received one day late
will be given a maximum 50% grade, and problem sets returned two or more days late will not be
graded.
Course Description:
Currently biology is undergoing a revolution whereby quantitative experimentation is providing
remarkable molecular details of the basic processes of life. In particular, recent advances in imaging
methods enable the visualization of collective interactions, while single molecule techniques can probe
specific molecular species. These experimental advances afford the perfect opportunity for synergy
between theory and experiments. This course will present an introduction to numerical methods that
are appropriate for modeling biological systems at various length and time scales. The aim will be to
provide experimentalists and theorists with an appreciation of both the possibilities and limitations of
these techniques. Our modeling efforts will range in resolution from examining enzyme motions at the
atomistic level to organismal development at the cellular level to large-scale population dynamics. To
develop and solve these models we will develop and use techniques such as molecular dynamics,
Monte Carlo simulations, and numerical solutions of differential equations.
Course Outline
1. Introduction and motivation for numerical modeling of biological systems (1)
2. Molecular interactions and dynamics (1-4)
-The origin of forces and motions that make biology work
-Newton's Laws and the equations of motion
-Introduction to MATLAB and programming
-Molecular dynamics simulation of neutral atoms
Cell biology:
B. Alberts et. al., Essential Cell Biology (Garland Science, 2003) ISBN 081533480X
Thermodynamics and statistical mechanics with an emphasis on biological systems:
K. Dill and S. Bromberg, Molecular Driving Forces,(Garland Science, 2003) ISBN 0815320515
P. Nelson, Biological Physics, (Freeman and Co., 2004) ISBN 0-7167-4372-8.
Dynamical systems analysis in biological systems:
Stephen P. Ellner & John Guckenheimer, Dynamic models in biology, (Princeton University
press, 2006) ISBN 9780691118437
C. P. Fall et. al., Computational Cell Biology (Springer, 2002) ISBN 0-387-95369-8
An interesting and informative presentation of probability accessible to all backgrounds:
V. Ambegaokar, Reasoning About Luck, (Cambridge, 1996) ISBN 0521447372